Variant report

Variant	rs2172530
Chromosome Location	chr5:1835083-1835084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1831073..1835336-chr5:1866302..1869597,4	MCF-7	breast:
2	chr5:1797383..1801692-chr5:1833304..1835855,5	MCF-7	breast:
3	chr5:1830290..1836159-chr5:1836315..1840959,6	MCF-7	breast:
4	chr5:1834384..1837437-chr5:1881304..1884006,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10074291	0.90[ASN][1000 genomes]
rs10475109	0.90[ASN][1000 genomes]
rs10866526	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs11739312	0.89[ASN][1000 genomes]
rs11740602	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11740753	0.84[EUR][1000 genomes]
rs11741881	0.91[CEU][hapmap];0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11748427	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11750565	0.84[EUR][1000 genomes]
rs1546252	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs1546253	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs17535295	0.81[ASN][1000 genomes]
rs17535337	0.86[CHB][hapmap]
rs17535721	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs2131588	0.95[CEU][hapmap];0.92[CHB][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131589	0.91[CEU][hapmap];0.93[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353585	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752844	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3756344	0.84[EUR][1000 genomes]
rs3776152	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3776154	0.81[EUR][1000 genomes]
rs4147775	0.84[EUR][1000 genomes]
rs4275010	0.81[ASN][1000 genomes]
rs4277951	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4296838	0.81[ASN][1000 genomes]
rs4296839	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4304110	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4416633	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4588629	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs60542979	0.83[EUR][1000 genomes]
rs62338060	0.90[ASN][1000 genomes]
rs62338061	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62338062	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6859338	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6862914	0.81[ASN][1000 genomes]
rs6864281	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6868515	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs6873986	0.91[CEU][hapmap];0.93[CHB][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6880885	0.81[ASN][1000 genomes]
rs6881253	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs6890404	0.81[ASN][1000 genomes]
rs6894566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701970	0.90[ASN][1000 genomes]
rs7703762	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7714300	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv461911	chr5:1820557-1855301	Strong transcription Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv596890	chr5:1820557-1855301	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2172530	MRPL36	cis	Muscle Skeletal	GTEx
rs2172530	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs2172530	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1827000-1836800	Weak transcription	Gastric	stomach
2	chr5:1827600-1854000	Weak transcription	Right Atrium	heart
3	chr5:1828600-1836800	Weak transcription	Spleen	Spleen
4	chr5:1831000-1835200	Enhancers	Fetal Heart	heart
5	chr5:1832400-1835200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:1832800-1836400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:1833600-1835400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:1833800-1836000	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr5:1834000-1835200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:1834000-1835800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr5:1834200-1835200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:1834200-1835200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:1834200-1835200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr5:1834200-1835400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:1834200-1835400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:1834400-1835200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:1834400-1835200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:1834400-1835400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:1834400-1835400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:1834400-1835600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:1834600-1836600	Weak transcription	Left Ventricle	heart
22	chr5:1834600-1837000	Weak transcription	Right Ventricle	heart
23	chr5:1834800-1835200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:1834800-1841400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:1835000-1835200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr5:1835000-1835200	Bivalent Enhancer	Brain Germinal Matrix	brain

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